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CrAssphage may be viable markers of contamination in pristine and contaminated river water
Mafumo, Nyasha; Bezuidt, Keoagile Ignatius Oliver; Le Roux, Wouter Jacobus; Makhalanyane, Thulani Peter
Viruses are the most biologically abundant entities and may be ideal
indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic
ecosystem changes in rivers, leading to substantial shifts in chemical and biological
attributes. Here, we evaluate the viability of using the presence of crAssphage as
indicators of fecal contamination in South African rivers. Shotgun analysis revealed
diverse crAssphage viruses in these rivers, which are impacted by chemical and biological
pollution. Overall, the diversity and relative abundances of these viruses was
higher in contaminated sites compared to pristine locations. In contrast to fecal coliform
counts, crAssphage sequences were detected in pristine rivers, supporting the
assertion that the afore mentioned marker may be a more accurate indicator of fecal
contamination. Our data demonstrate the presence of diverse putative hosts which
includes members of the phyla Bacteroidota, Pseudomonadota, Verrucomicrobiota,
and Bacillota. Phylogenetic analysis revealed novel subfamilies, suggesting that rivers
potentially harbor distinct and uncharacterized clades of crAssphage. These data provide
the first insights regarding the diversity, distribution, and functional roles of
crAssphage in rivers. Taken together, the results support the potential application of
crAssphage as viable markers for water quality monitoring.
IMPORTANCE : Rivers support substantial populations and provide important ecosystem
services. Despite the application of fecal coliform tests and other markers, we
lack rapid and reproducible approaches for determining fecal contamination in rivers.
Waterborne viral outbreaks have been reported even after fecal indicator bacteria
(FIB) were suggested to be absent or below regulated levels of coliforms. This
indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination
in two South African rivers. We assess the abundance, distribution, and
diversity of these viruses in sites that had been predicted pristine or contaminated
by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal
contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies
were unrepresented in our data, suggesting that the diversity of these
viruses may reflect geographic locality and dependence.
Description:
DATA AVAILABILITY. The metagenomic data have been deposited at NCBI under BioProject ID
PRJNA894350. Metagenomic assembled genomes are available from https://doi.org/10.6084/m9.figshare
.21640316. The bash script and HMM profiles used to search for crAss-like viruses in our data can be
accessed from https://github.com/SAmicrobiomes/crAssZA.